The man, 72, and his 71-year-old wife have not been named.
An investigation was launched after a suitcase with some of the woman's body parts was found by a man walking near Traunsee lake on Sunday.
A day later, the German man's body was found in 5m (15ft) of water, with his wrists weighed down by bags of stones.
Investigators on Tuesday said the head of his wife, encased in concrete, was found near the man's body in the lake near the town of Gmunden, 80km (50 miles) east of Salzburg. Read more on bbc.